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<div class="title">particle_dynamics_diffusion_reaction.h</div>  </div>
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<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">/* -------------------------------------------------------------------------*</span></div><div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">*                               SPHinXsys                                   *</span></div><div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">* --------------------------------------------------------------------------*</span></div><div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">* SPHinXsys (pronunciation: s&#39;finksis) is an acronym from Smoothed Particle *</span></div><div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">* Hydrodynamics for industrial compleX systems. It provides C++ APIs for    *</span></div><div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">* physical accurate simulation and aims to model coupled industrial dynamic *</span></div><div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">* systems including fluid, solid, multi-body dynamics and beyond with SPH   *</span></div><div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">* (smoothed particle hydrodynamics), a meshless computational method using  *</span></div><div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">* particle discretization.                                                  *</span></div><div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="comment">*                                                                           *</span></div><div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="comment">* SPHinXsys is partially funded by German Research Foundation               *</span></div><div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment">* (Deutsche Forschungsgemeinschaft) DFG HU1527/6-1, HU1527/10-1             *</span></div><div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="comment">* and HU1527/12-1.                                                          *</span></div><div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">*                                                                           *</span></div><div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="comment">* Portions copyright (c) 2017-2020 Technical University of Munich and       *</span></div><div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="comment">* the authors&#39; affiliations.                                                *</span></div><div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">*                                                                           *</span></div><div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">* Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may   *</span></div><div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment">* not use this file except in compliance with the License. You may obtain a *</span></div><div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="comment">* copy of the License at http://www.apache.org/licenses/LICENSE-2.0.        *</span></div><div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="comment">*                                                                           *</span></div><div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="comment">* --------------------------------------------------------------------------*/</span></div><div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="preprocessor">#pragma once</span></div><div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;</div><div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;<span class="preprocessor">#include &quot;all_particle_dynamics.h&quot;</span></div><div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="diffusion__reaction__particles_8h.html">diffusion_reaction_particles.h</a>&quot;</span></div><div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;<span class="preprocessor">#include &quot;diffusion_reaction.h&quot;</span></div><div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;</div><div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;</div><div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;<span class="keyword">namespace </span><a class="code" href="namespace_s_p_h.html">SPH</a></div><div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;{</div><div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;    <span class="keyword">using</span> DiffusionBase = ParticleDynamics&lt;<a class="code" href="class_real.html">Real</a>, BodyType,</div><div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;        DiffusionReactionParticles&lt;BaseParticlesType, BaseMaterialType&gt;, DiffusionReactionMaterial&lt;BaseParticlesType, BaseMaterialType&gt;&gt;;</div><div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;</div><div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;    <span class="keyword">using</span> DiffusionReactionSimple = ParticleDynamicsSimple&lt;BodyType,</div><div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;        DiffusionReactionParticles&lt;BaseParticlesType, BaseMaterialType&gt;, DiffusionReactionMaterial&lt;BaseParticlesType, BaseMaterialType&gt;&gt;;</div><div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;</div><div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;    <span class="keyword">using</span> DiffusionInner = ParticleDynamicsInner&lt;BodyType,</div><div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;        DiffusionReactionParticles&lt;BaseParticlesType, BaseMaterialType&gt;, DiffusionReactionMaterial&lt;BaseParticlesType, BaseMaterialType&gt;&gt;;</div><div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;</div><div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;    <span class="keyword">using</span> DiffusionInnerWithUpdate = ParticleDynamicsInnerWithUpdate&lt;BodyType,</div><div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;        DiffusionReactionParticles&lt;BaseParticlesType, BaseMaterialType&gt;, DiffusionReactionMaterial&lt;BaseParticlesType, BaseMaterialType&gt;&gt;;</div><div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;</div><div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BodyPartByParticleType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;    <span class="keyword">using</span> DiffusionReactionConstraint = PartDynamicsByParticle&lt;BodyType,</div><div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;        DiffusionReactionParticles&lt;BaseParticlesType, BaseMaterialType&gt;, BodyPartByParticleType, </div><div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;        DiffusionReactionMaterial&lt;BaseParticlesType, BaseMaterialType&gt;&gt;;</div><div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;</div><div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00079"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_get_diffusion_time_step_size.html">   79</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_get_diffusion_time_step_size.html">GetDiffusionTimeStepSize</a></div><div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;        : <span class="keyword">public</span>  <a class="code" href="class_s_p_h_1_1_particle_dynamics.html">DiffusionBase</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div><div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;    {</div><div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;        Real diff_time_step_;</div><div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;        <span class="keyword">explicit</span> <a class="code" href="class_s_p_h_1_1_get_diffusion_time_step_size.html">GetDiffusionTimeStepSize</a>(BodyType* body)</div><div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;            : <a class="code" href="class_s_p_h_1_1_particle_dynamics.html">DiffusionBase&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</a>(body) </div><div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;        {</div><div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;            Real smoothing_length = body-&gt;kernel_-&gt;GetSmoothingLength();</div><div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;            diff_time_step_ = this-&gt;material_-&gt;getDiffusionTimeStepSize(smoothing_length);</div><div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;        };</div><div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_get_diffusion_time_step_size.html">GetDiffusionTimeStepSize</a>() {};</div><div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;</div><div class="line"><a name="l00093"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_get_diffusion_time_step_size.html#abbafdb225bf35578cb3d8d891f54b1e9">   93</a></span>&#160;        <span class="keyword">virtual</span> Real <a class="code" href="class_s_p_h_1_1_get_diffusion_time_step_size.html#abbafdb225bf35578cb3d8d891f54b1e9">exec</a>(Real dt = 0.0)<span class="keyword"> override </span>{ <span class="keywordflow">return</span> diff_time_step_; };</div><div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;        <span class="keyword">virtual</span> Real parallel_exec(Real dt = 0.0)<span class="keyword"> override </span>{ <span class="keywordflow">return</span> <a class="code" href="class_s_p_h_1_1_get_diffusion_time_step_size.html#abbafdb225bf35578cb3d8d891f54b1e9">exec</a>(dt); };</div><div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;    };</div><div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;</div><div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00102"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_difussion_species.html">  102</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_relaxation_of_all_difussion_species.html">RelaxationOfAllDifussionSpecies</a></div><div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;        : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_particle_dynamics_inner_with_update.html">DiffusionInnerWithUpdate</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div><div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;    {</div><div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;        StdVec&lt;BaseDiffusion*&gt; species_diffusion_;</div><div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00112"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_difussion_species.html#ad1cd798d759a665cc40131c773aa581f">  112</a></span>&#160;        <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_relaxation_of_all_difussion_species.html#ad1cd798d759a665cc40131c773aa581f">initializeDiffusionChangeRate</a>(<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html">DiffusionReactionData</a>&amp; diffusion_reaction_data_i)</div><div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;        {</div><div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;            <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> m = 0; m &lt; species_diffusion_.size(); ++m)</div><div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;            {</div><div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;                <span class="keywordtype">size_t</span> k = species_diffusion_[m]-&gt;diffusion_species_index_;</div><div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;                diffusion_reaction_data_i.<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html#a9c9c5fa76e83b20f66c7eb961dea9b76">dspecies_dt_</a>[k] = 0;</div><div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;            }</div><div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;        };</div><div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;</div><div class="line"><a name="l00130"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_difussion_species.html#ab82d1578c5e8cbabe687e0af9810fbd1">  130</a></span>&#160;        <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_relaxation_of_all_difussion_species.html#ab82d1578c5e8cbabe687e0af9810fbd1">getDiffusionChangeRate</a>(<span class="keywordtype">size_t</span> particle_i, <span class="keywordtype">size_t</span> particle_j, Vecd&amp; e_ij, Real surface_area_ij,</div><div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;            <a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html">DiffusionReactionData</a>&amp; diffusion_reaction_data_i, <a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html">DiffusionReactionData</a>&amp; diffusion_reaction_data_j)</div><div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;        {</div><div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;            <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> m = 0; m &lt; species_diffusion_.size(); ++m)</div><div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;            {</div><div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;                Real diff_coff_ij = species_diffusion_[m]-&gt;getInterParticleDiffusionCoff(particle_i, particle_j, e_ij);</div><div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;                <span class="keywordtype">size_t</span> k = species_diffusion_[m]-&gt;diffusion_species_index_;</div><div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;                <span class="keywordtype">size_t</span> l = species_diffusion_[m]-&gt;gradient_species_index_;</div><div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;                Real phi_ij = diffusion_reaction_data_i.<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html#a387eae85205f80dd35b898faee438ad5">species_n_</a>[l] - diffusion_reaction_data_j.<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html#a387eae85205f80dd35b898faee438ad5">species_n_</a>[l];</div><div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;                diffusion_reaction_data_i.<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html#a9c9c5fa76e83b20f66c7eb961dea9b76">dspecies_dt_</a>[k] += diff_coff_ij * phi_ij * surface_area_ij;</div><div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;            }</div><div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;        };</div><div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;</div><div class="line"><a name="l00148"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_difussion_species.html#a0e202b2a607b21d6c94075270217c852">  148</a></span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_relaxation_of_all_difussion_species.html#a0e202b2a607b21d6c94075270217c852">updateDiffusionSpecies</a>(<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html">DiffusionReactionData</a>&amp; diffusion_reaction_data_i, Real dt)</div><div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;        {</div><div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;            <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> m = 0; m &lt; species_diffusion_.size(); ++m)</div><div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;            {</div><div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;                <span class="keywordtype">size_t</span> k = species_diffusion_[m]-&gt;diffusion_species_index_;</div><div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;                diffusion_reaction_data_i.<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html#a387eae85205f80dd35b898faee438ad5">species_n_</a>[k] += dt * diffusion_reaction_data_i.<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html#a9c9c5fa76e83b20f66c7eb961dea9b76">dspecies_dt_</a>[k];</div><div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;            }</div><div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;        };</div><div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;</div><div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> InnerInteraction(<span class="keywordtype">size_t</span> index_particle_i, Real dt = 0.0)<span class="keyword"> override</span></div><div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;<span class="keyword">        </span>{</div><div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;            <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html">DiffusionReactionParticles&lt;BaseParticlesType, BaseMaterialType&gt;</a>* particles = this-&gt;particles_;</div><div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;            <a class="code" href="class_s_p_h_1_1_neighborhood.html">Neighborhood</a>&amp; inner_neighborhood = this-&gt;<a class="code" href="class_s_p_h_1_1_particle_dynamics_with_inner_configurations.html#a847144aa189dd161047be589b5b59507">inner_configuration_</a>[index_particle_i];</div><div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;</div><div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;            StdLargeVec&lt;DiffusionReactionData&gt;&amp; diffusion_reaction_data = particles-&gt;<a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#ace9886026ada5948e27c14a0ce827b2f">diffusion_reaction_data_</a>;</div><div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;            StdLargeVec&lt;BaseParticleData&gt;&amp; base_particle_data = particles-&gt;base_particle_data_;</div><div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;            <a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html">DiffusionReactionData</a>&amp; diffusion_reaction_data_i = diffusion_reaction_data[index_particle_i];</div><div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;</div><div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;            <a class="code" href="class_s_p_h_1_1_relaxation_of_all_difussion_species.html#ad1cd798d759a665cc40131c773aa581f">initializeDiffusionChangeRate</a>(diffusion_reaction_data_i);</div><div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;            <a class="code" href="namespace_s_p_h.html#aa1b1a469a853a78ec95f6bf7b3ded9f4">CommonRelationList</a>&amp; inner_common_relations = inner_neighborhood.common_relation_list_;</div><div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;            <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> n = 0; n != inner_neighborhood.<a class="code" href="class_s_p_h_1_1_neighborhood.html#a1e2d0d9c7af09e2ee0e58903b171902d">current_size_</a>; ++n)</div><div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;            {</div><div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;                <a class="code" href="class_s_p_h_1_1_common_relation.html">CommonRelation</a>&amp; common_relation = inner_common_relations[n];</div><div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;                <span class="keywordtype">size_t</span> index_particle_j = common_relation.<a class="code" href="class_s_p_h_1_1_common_relation.html#a7c8fa7c04fd21a9668feade22912115b">j_</a>;</div><div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;                Vecd&amp; e_ij = common_relation.<a class="code" href="class_s_p_h_1_1_common_relation.html#a3e4dd95b6dbe984aeb19c2e4977fd161">e_ij_</a>;</div><div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;                <a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html">DiffusionReactionData</a>&amp; diffusion_reaction_data_j = diffusion_reaction_data[index_particle_j];</div><div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;    </div><div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;                <span class="keyword">const</span> Vecd&amp; gradi_ij = particles-&gt;getKernelGradient(index_particle_i, index_particle_j, common_relation.<a class="code" href="class_s_p_h_1_1_common_relation.html#a2fdbf618dfaaca3cf77176907c1e7ae0">dW_ij_</a>, e_ij);</div><div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;                Real area_ij = 2.0 * base_particle_data[index_particle_j].Vol_ * dot(gradi_ij, e_ij) / common_relation.<a class="code" href="class_s_p_h_1_1_common_relation.html#a1a3bacd903ac2c946e196610b634bcaf">r_ij_</a>;</div><div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;                <a class="code" href="class_s_p_h_1_1_relaxation_of_all_difussion_species.html#ab82d1578c5e8cbabe687e0af9810fbd1">getDiffusionChangeRate</a>(index_particle_i, index_particle_j, e_ij, area_ij,</div><div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;                    diffusion_reaction_data_i, diffusion_reaction_data_j);</div><div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;            }</div><div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;        };</div><div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;</div><div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> Update(<span class="keywordtype">size_t</span> index_particle_i, <a class="code" href="class_real.html">Real</a> dt = 0.0)<span class="keyword"> override </span></div><div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;<span class="keyword">        </span>{</div><div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;            DiffusionReactionParticles&lt;BaseParticlesType, BaseMaterialType&gt;* particles = this-&gt;particles_;</div><div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;            StdLargeVec&lt;DiffusionReactionData&gt;&amp; diffusion_reaction_data = particles-&gt;diffusion_reaction_data_;</div><div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;            DiffusionReactionData&amp; diffusion_reaction_data_i = diffusion_reaction_data[index_particle_i];</div><div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;            <a class="code" href="class_s_p_h_1_1_relaxation_of_all_difussion_species.html#a0e202b2a607b21d6c94075270217c852">updateDiffusionSpecies</a>(diffusion_reaction_data_i, dt);</div><div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;        };</div><div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;        RelaxationOfAllDifussionSpecies(SPHBodyInnerRelation* body_inner_relation)</div><div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;            : DiffusionInnerWithUpdate&lt;BodyType, <a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>, <a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>&gt;(body_inner_relation) {</div><div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;            species_diffusion_ = this-&gt;material_-&gt;getDiffusionSpecies();</div><div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;        };</div><div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;        <span class="keyword">virtual</span> ~RelaxationOfAllDifussionSpecies() {};</div><div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;    };</div><div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;</div><div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00203"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html">  203</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html">RelaxationOfAllDiffusionSpeciesRK2</a></div><div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;        : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_particle_dynamics.html">ParticleDynamics</a>&lt;void, BodyType, BaseParticlesType, BaseMaterialType&gt;</div><div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;    {</div><div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;        <span class="keyword">template</span>&lt;<span class="keyword">class</span> ParameterBody, <span class="keyword">class</span> ParameterBaseParticles, <span class="keyword">class</span> ParameterBaseMaterial&gt;</div><div class="line"><a name="l00208"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_1_1_runge_kutta_initialization.html">  208</a></span>&#160;        <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_1_1_runge_kutta_initialization.html">RungeKuttaInitialization</a> :</div><div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;            <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_particle_dynamics_simple.html">DiffusionReactionSimple</a>&lt;ParameterBody, ParameterBaseParticles, ParameterBaseMaterial&gt;</div><div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;        {</div><div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;            StdVec&lt;BaseDiffusion*&gt; species_diffusion_;</div><div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;        <span class="keyword">protected</span>:</div><div class="line"><a name="l00213"></a><span class="lineno">  213</span>&#160;</div><div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;            <span class="keywordtype">void</span> initializeIntermediateValue(<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html">DiffusionReactionData</a>&amp; diffusion_reaction_data_i)</div><div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;            {</div><div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;                <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> m = 0; m &lt; species_diffusion_.size(); ++m)</div><div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;                {</div><div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;                    <span class="keywordtype">size_t</span> k = species_diffusion_[m]-&gt;diffusion_species_index_;</div><div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;                    diffusion_reaction_data_i.<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html#a225749466f115c22bae74deb18140ce7">species_s_</a>[k] = diffusion_reaction_data_i.<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html#a387eae85205f80dd35b898faee438ad5">species_n_</a>[k];</div><div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;                }</div><div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;            };</div><div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;</div><div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;            <span class="keyword">virtual</span> <span class="keywordtype">void</span> Update(<span class="keywordtype">size_t</span> index_particle_i, Real dt = 0.0)<span class="keyword"> override </span></div><div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;<span class="keyword">            </span>{</div><div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;                <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html">DiffusionReactionParticles&lt;ParameterBaseParticles, ParameterBaseMaterial&gt;</a>* particles = this-&gt;particles_;</div><div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;                StdLargeVec&lt;DiffusionReactionData&gt;&amp; diffusion_reaction_data = particles-&gt;<a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#ace9886026ada5948e27c14a0ce827b2f">diffusion_reaction_data_</a>;</div><div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;                <a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html">DiffusionReactionData</a>&amp; diffusion_reaction_data_i = diffusion_reaction_data[index_particle_i];</div><div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;                initializeIntermediateValue(diffusion_reaction_data_i);</div><div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;            };</div><div class="line"><a name="l00230"></a><span class="lineno">  230</span>&#160;        <span class="keyword">public</span>:</div><div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;            <a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_1_1_runge_kutta_initialization.html">RungeKuttaInitialization</a>(<a class="code" href="class_s_p_h_1_1_s_p_h_body.html">SPHBody</a>* body)</div><div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;                : <a class="code" href="class_s_p_h_1_1_particle_dynamics_simple.html">DiffusionReactionSimple&lt;ParameterBody, ParameterBaseParticles, ParameterBaseMaterial&gt;</a>(body) </div><div class="line"><a name="l00233"></a><span class="lineno">  233</span>&#160;            {</div><div class="line"><a name="l00234"></a><span class="lineno">  234</span>&#160;                species_diffusion_ = this-&gt;material_-&gt;getDiffusionSpecies();</div><div class="line"><a name="l00235"></a><span class="lineno">  235</span>&#160; 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       {</div><div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;            StdVec&lt;BaseDiffusion*&gt; species_diffusion_;</div><div class="line"><a name="l00243"></a><span class="lineno">  243</span>&#160;        <span class="keyword">protected</span>:</div><div class="line"><a name="l00244"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_1_1_runge_kutta2_stages2nd_stage.html#a93084988dfa7a46c43ef5e899e2e1b06">  244</a></span>&#160;            <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_1_1_runge_kutta2_stages2nd_stage.html#a93084988dfa7a46c43ef5e899e2e1b06">updateDiffusionSpecies</a>(<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html">DiffusionReactionData</a>&amp; diffusion_reaction_data_i, Real dt)<span class="keyword"> override</span></div><div class="line"><a name="l00245"></a><span class="lineno">  245</span>&#160;<span class="keyword">            </span>{</div><div class="line"><a name="l00246"></a><span class="lineno">  246</span>&#160;                <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> m = 0; m &lt; species_diffusion_.size(); ++m)</div><div class="line"><a name="l00247"></a><span class="lineno">  247</span>&#160;                {</div><div class="line"><a name="l00248"></a><span class="lineno">  248</span>&#160;                    <span class="keywordtype">size_t</span> k = species_diffusion_[m]-&gt;diffusion_species_index_;</div><div class="line"><a name="l00249"></a><span class="lineno">  249</span>&#160;                    diffusion_reaction_data_i.<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html#a387eae85205f80dd35b898faee438ad5">species_n_</a>[k] = 0.5 * diffusion_reaction_data_i.<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html#a225749466f115c22bae74deb18140ce7">species_s_</a>[k]</div><div class="line"><a name="l00250"></a><span class="lineno">  250</span>&#160;                    + 0.5 * (diffusion_reaction_data_i.<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html#a387eae85205f80dd35b898faee438ad5">species_n_</a>[k] + dt * diffusion_reaction_data_i.<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html#a9c9c5fa76e83b20f66c7eb961dea9b76">dspecies_dt_</a>[k]);</div><div class="line"><a name="l00251"></a><span class="lineno">  251</span>&#160;                }</div><div class="line"><a name="l00252"></a><span class="lineno">  252</span>&#160;            };</div><div class="line"><a name="l00253"></a><span class="lineno">  253</span>&#160;        <span class="keyword">public</span>:</div><div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;            <a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_1_1_runge_kutta2_stages2nd_stage.html">RungeKutta2Stages2ndStage</a>(<a class="code" href="class_s_p_h_1_1_s_p_h_body_inner_relation.html">SPHBodyInnerRelation</a>* body_inner_relation)</div><div class="line"><a name="l00255"></a><span class="lineno">  255</span>&#160;                : <a class="code" href="class_s_p_h_1_1_relaxation_of_all_difussion_species.html">RelaxationOfAllDifussionSpecies</a>&lt;ParameterBody, ParameterBaseParticles, ParameterBaseMaterial&gt;(body_inner_relation)</div><div class="line"><a name="l00256"></a><span class="lineno">  256</span>&#160;            {</div><div class="line"><a name="l00257"></a><span class="lineno">  257</span>&#160;                species_diffusion_ = this-&gt;material_-&gt;getDiffusionSpecies();</div><div class="line"><a name="l00258"></a><span class="lineno">  258</span>&#160;            };</div><div class="line"><a name="l00259"></a><span class="lineno">  259</span>&#160;            <span class="keyword">virtual</span> ~RungeKutta2Stages2ndStage() {};</div><div class="line"><a name="l00260"></a><span class="lineno">  260</span>&#160;        };</div><div class="line"><a name="l00261"></a><span class="lineno">  261</span>&#160;</div><div class="line"><a name="l00262"></a><span class="lineno">  262</span>&#160;        RungeKuttaInitialization&lt;BodyType, BaseParticlesType, BaseMaterialType&gt; runge_kutta_initialization_;</div><div class="line"><a name="l00263"></a><span class="lineno">  263</span>&#160;        RelaxationOfAllDifussionSpecies&lt;BodyType, BaseParticlesType, BaseMaterialType&gt; runge_kutta_1st_stage_;</div><div class="line"><a name="l00264"></a><span class="lineno">  264</span>&#160;        RungeKutta2Stages2ndStage&lt;BodyType, BaseParticlesType, BaseMaterialType&gt; runge_kutta_2nd_stage_;</div><div class="line"><a name="l00265"></a><span class="lineno">  265</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00266"></a><span class="lineno">  266</span>&#160;        RelaxationOfAllDiffusionSpeciesRK2(SPHBodyInnerRelation* body_inner_relation)</div><div class="line"><a name="l00267"></a><span class="lineno">  267</span>&#160;            : <a class="code" href="class_s_p_h_1_1_particle_dynamics.html#a129036fc16e69eb21e69a259ca20036a">ParticleDynamics</a>&lt;void, BodyType, <a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>, <a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>&gt;(body_inner_relation-&gt;body_),</div><div class="line"><a name="l00268"></a><span class="lineno">  268</span>&#160;            runge_kutta_initialization_(body_inner_relation-&gt;body_), runge_kutta_1st_stage_(body_inner_relation),</div><div class="line"><a name="l00269"></a><span class="lineno">  269</span>&#160;            runge_kutta_2nd_stage_(body_inner_relation){};</div><div class="line"><a name="l00270"></a><span class="lineno">  270</span>&#160;        <span class="keyword">virtual</span> ~RelaxationOfAllDiffusionSpeciesRK2() {};</div><div class="line"><a name="l00271"></a><span class="lineno">  271</span>&#160;</div><div class="line"><a name="l00272"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html#ac90349521ec2a782159bb2536722e3bb">  272</a></span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html#ac90349521ec2a782159bb2536722e3bb">exec</a>(Real dt = 0.0)<span class="keyword"> override </span>{</div><div class="line"><a name="l00273"></a><span class="lineno">  273</span>&#160;            runge_kutta_initialization_.exec();</div><div class="line"><a name="l00274"></a><span class="lineno">  274</span>&#160;            runge_kutta_1st_stage_.exec(dt);</div><div class="line"><a name="l00275"></a><span class="lineno">  275</span>&#160;            runge_kutta_2nd_stage_.exec(dt);</div><div class="line"><a name="l00276"></a><span class="lineno">  276</span>&#160;        };</div><div class="line"><a name="l00277"></a><span class="lineno">  277</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> parallel_exec(Real dt = 0.0)<span class="keyword"> override </span>{</div><div class="line"><a name="l00278"></a><span class="lineno">  278</span>&#160;            runge_kutta_initialization_.parallel_exec();</div><div class="line"><a name="l00279"></a><span class="lineno">  279</span>&#160;            runge_kutta_1st_stage_.parallel_exec(dt);</div><div class="line"><a name="l00280"></a><span class="lineno">  280</span>&#160;            runge_kutta_2nd_stage_.parallel_exec(dt);</div><div class="line"><a name="l00281"></a><span class="lineno">  281</span>&#160;        };</div><div class="line"><a name="l00282"></a><span class="lineno">  282</span>&#160;    };</div><div class="line"><a name="l00283"></a><span class="lineno">  283</span>&#160;</div><div class="line"><a name="l00288"></a><span class="lineno">  288</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00289"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_reactions_foward.html">  289</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_relaxation_of_all_reactions_foward.html">RelaxationOfAllReactionsFoward</a> :</div><div class="line"><a name="l00290"></a><span class="lineno">  290</span>&#160;        <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_particle_dynamics_simple.html">DiffusionReactionSimple</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div><div class="line"><a name="l00291"></a><span class="lineno">  291</span>&#160;    {</div><div class="line"><a name="l00293"></a><span class="lineno">  293</span>&#160;        <a class="code" href="class_s_p_h_1_1_base_reaction_model.html">BaseReactionModel</a>* species_reaction_;</div><div class="line"><a name="l00294"></a><span class="lineno">  294</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00303"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_reactions_foward.html#aceb02571347f79c52fb1b97870863a36">  303</a></span>&#160;        Real <a class="code" href="class_s_p_h_1_1_relaxation_of_all_reactions_foward.html#aceb02571347f79c52fb1b97870863a36">updateAReactionSpecies</a>(Real input, Real production_rate, Real loss_rate, Real dt)</div><div class="line"><a name="l00304"></a><span class="lineno">  304</span>&#160;        {</div><div class="line"><a name="l00305"></a><span class="lineno">  305</span>&#160;            <span class="keywordflow">return</span> input * exp(-loss_rate * dt) + production_rate * (1.0 - exp(-loss_rate * dt)) / (loss_rate + TinyReal);</div><div class="line"><a name="l00306"></a><span class="lineno">  306</span>&#160;        };</div><div class="line"><a name="l00312"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_reactions_foward.html#a343795cd46824a0595121c07a5480662">  312</a></span>&#160;        <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_relaxation_of_all_reactions_foward.html#a343795cd46824a0595121c07a5480662">UpdateReactiveSpeciesForward</a>(<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html">DiffusionReactionData</a>&amp; diffusion_reaction_data_i, Real dt) {</div><div class="line"><a name="l00313"></a><span class="lineno">  313</span>&#160;            <a class="code" href="namespace_s_p_h.html#abae56fd7f25f13487c7943ce4681d0ce">IndexVector</a>&amp; reactive_species = species_reaction_-&gt;<a class="code" href="class_s_p_h_1_1_base_reaction_model.html#a5d7b0f83c36dd9b3efd1c5a8c74f2073">reactive_species_</a>;</div><div class="line"><a name="l00314"></a><span class="lineno">  314</span>&#160;</div><div class="line"><a name="l00315"></a><span class="lineno">  315</span>&#160;            <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> m = 0; m != reactive_species.size(); ++m) {</div><div class="line"><a name="l00316"></a><span class="lineno">  316</span>&#160;                <span class="keywordtype">size_t</span> k = reactive_species[m];</div><div class="line"><a name="l00317"></a><span class="lineno">  317</span>&#160;                Real production_rate = species_reaction_-&gt;<a class="code" href="class_s_p_h_1_1_base_reaction_model.html#a910ab731d18d21e073360a0e837e9dc9">get_production_rates_</a>[k](diffusion_reaction_data_i.<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html#a387eae85205f80dd35b898faee438ad5">species_n_</a>);</div><div class="line"><a name="l00318"></a><span class="lineno">  318</span>&#160;                Real loss_rate = species_reaction_-&gt;<a class="code" href="class_s_p_h_1_1_base_reaction_model.html#ac9370e5551fc733dccfa12e9364bb27d">get_loss_rates_</a>[k](diffusion_reaction_data_i.<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html#a387eae85205f80dd35b898faee438ad5">species_n_</a>);</div><div class="line"><a name="l00319"></a><span class="lineno">  319</span>&#160;                Real input = diffusion_reaction_data_i.<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html#a387eae85205f80dd35b898faee438ad5">species_n_</a>[k];</div><div class="line"><a name="l00320"></a><span class="lineno">  320</span>&#160;                diffusion_reaction_data_i.<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html#a387eae85205f80dd35b898faee438ad5">species_n_</a>[k] = <a class="code" href="class_s_p_h_1_1_relaxation_of_all_reactions_foward.html#aceb02571347f79c52fb1b97870863a36">updateAReactionSpecies</a>(input, production_rate, loss_rate, dt);</div><div class="line"><a name="l00321"></a><span class="lineno">  321</span>&#160;            }</div><div class="line"><a name="l00322"></a><span class="lineno">  322</span>&#160;        };</div><div class="line"><a name="l00323"></a><span class="lineno">  323</span>&#160;</div><div class="line"><a name="l00324"></a><span class="lineno">  324</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> Update(<span class="keywordtype">size_t</span> index_particle_i, Real dt = 0.0)<span class="keyword"> override </span>{</div><div class="line"><a name="l00325"></a><span class="lineno">  325</span>&#160;            <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html">DiffusionReactionParticles&lt;BaseParticlesType, BaseMaterialType&gt;</a>* particles = this-&gt;particles_;</div><div class="line"><a name="l00326"></a><span class="lineno">  326</span>&#160;            <a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html">DiffusionReactionData</a>&amp; diffusion_reaction_data_i = particles-&gt;<a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#ace9886026ada5948e27c14a0ce827b2f">diffusion_reaction_data_</a>[index_particle_i];</div><div class="line"><a name="l00327"></a><span class="lineno">  327</span>&#160;            <a class="code" href="class_s_p_h_1_1_relaxation_of_all_reactions_foward.html#a343795cd46824a0595121c07a5480662">UpdateReactiveSpeciesForward</a>(diffusion_reaction_data_i, dt);</div><div class="line"><a name="l00328"></a><span class="lineno">  328</span>&#160;        };</div><div class="line"><a name="l00329"></a><span class="lineno">  329</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00330"></a><span class="lineno">  330</span>&#160;        RelaxationOfAllReactionsFoward(BodyType* body)</div><div class="line"><a name="l00331"></a><span class="lineno">  331</span>&#160;            : DiffusionReactionSimple&lt;BodyType, <a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>, <a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>&gt;(body) {</div><div class="line"><a name="l00332"></a><span class="lineno">  332</span>&#160;            species_reaction_ = this-&gt;material_-&gt;getReactionModel();</div><div class="line"><a name="l00333"></a><span class="lineno">  333</span>&#160;        };</div><div class="line"><a name="l00334"></a><span class="lineno">  334</span>&#160;        <span class="keyword">virtual</span> ~RelaxationOfAllReactionsFoward() {};</div><div class="line"><a name="l00335"></a><span class="lineno">  335</span>&#160;    };</div><div class="line"><a name="l00336"></a><span class="lineno">  336</span>&#160;</div><div class="line"><a name="l00341"></a><span class="lineno">  341</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00342"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_reactions_backward.html">  342</a></span>&#160; 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diffusion_reaction_data_i, Real dt)</div><div class="line"><a name="l00367"></a><span class="lineno">  367</span>&#160;        {</div><div class="line"><a name="l00368"></a><span class="lineno">  368</span>&#160;            <a class="code" href="namespace_s_p_h.html#abae56fd7f25f13487c7943ce4681d0ce">IndexVector</a>&amp; reactive_species = species_reaction_-&gt;<a class="code" href="class_s_p_h_1_1_base_reaction_model.html#a5d7b0f83c36dd9b3efd1c5a8c74f2073">reactive_species_</a>;</div><div class="line"><a name="l00369"></a><span class="lineno">  369</span>&#160;</div><div class="line"><a name="l00370"></a><span class="lineno">  370</span>&#160;            <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> m = reactive_species.size(); m != 0; --m) {</div><div class="line"><a name="l00371"></a><span class="lineno">  371</span>&#160;                <span class="keywordtype">size_t</span> k = reactive_species[m - 1];</div><div class="line"><a name="l00372"></a><span class="lineno">  372</span>&#160; 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               diffusion_reaction_data_i.<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html#a387eae85205f80dd35b898faee438ad5">species_n_</a>[k] = <a class="code" href="class_s_p_h_1_1_relaxation_of_all_reactions_backward.html#a70a0ba2530a5fc9bc2e99340b36ba00c">updateAReactionSpecies</a>(input, production_rate, loss_rate, dt);</div><div class="line"><a name="l00376"></a><span class="lineno">  376</span>&#160;            }</div><div class="line"><a name="l00377"></a><span class="lineno">  377</span>&#160;        };</div><div class="line"><a name="l00378"></a><span class="lineno">  378</span>&#160;</div><div class="line"><a name="l00379"></a><span class="lineno">  379</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> Update(<span class="keywordtype">size_t</span> index_particle_i, Real dt = 0.0)<span class="keyword"> override</span></div><div class="line"><a name="l00380"></a><span class="lineno">  380</span>&#160;<span class="keyword">        </span>{</div><div class="line"><a name="l00381"></a><span class="lineno">  381</span>&#160;            <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html">DiffusionReactionParticles&lt;BaseParticlesType, BaseMaterialType&gt;</a>* particles = this-&gt;particles_;</div><div class="line"><a name="l00382"></a><span class="lineno">  382</span>&#160;            <a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html">DiffusionReactionData</a>&amp; diffusion_reaction_data_i = particles-&gt;<a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#ace9886026ada5948e27c14a0ce827b2f">diffusion_reaction_data_</a>[index_particle_i];</div><div class="line"><a name="l00383"></a><span class="lineno">  383</span>&#160;            <a class="code" href="class_s_p_h_1_1_relaxation_of_all_reactions_backward.html#a7274653cfb4e8a753476dd247990f206">UpdateReactiveSpeciesBackward</a>(diffusion_reaction_data_i, dt);</div><div class="line"><a name="l00384"></a><span class="lineno">  384</span>&#160;        };</div><div class="line"><a name="l00385"></a><span class="lineno">  385</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00386"></a><span class="lineno">  386</span>&#160;        RelaxationOfAllReactionsBackward(BodyType* body)</div><div class="line"><a name="l00387"></a><span class="lineno">  387</span>&#160;            : DiffusionReactionSimple&lt;BodyType, <a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>, <a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>&gt;(body) </div><div class="line"><a name="l00388"></a><span class="lineno">  388</span>&#160;        {</div><div class="line"><a name="l00389"></a><span class="lineno">  389</span>&#160;            species_reaction_ = this-&gt;material_-&gt;getReactionModel();</div><div class="line"><a name="l00390"></a><span class="lineno">  390</span>&#160;        };</div><div class="line"><a name="l00391"></a><span class="lineno">  391</span>&#160;        <span class="keyword">virtual</span> ~RelaxationOfAllReactionsBackward() {};</div><div class="line"><a name="l00392"></a><span class="lineno">  392</span>&#160;    };</div><div class="line"><a name="l00397"></a><span class="lineno">  397</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BodyPartByParticleType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00398"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_boundary_condtion.html">  398</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_diffusion_boundary_condtion.html">DiffusionBoundaryCondtion</a> :</div><div class="line"><a name="l00399"></a><span class="lineno">  399</span>&#160;        <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_part_dynamics_by_particle.html">DiffusionReactionConstraint</a>&lt;BodyType, BaseParticlesType, BodyPartByParticleType, BaseMaterialType&gt;</div><div class="line"><a name="l00400"></a><span class="lineno">  400</span>&#160;    {</div><div class="line"><a name="l00401"></a><span class="lineno">  401</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00402"></a><span class="lineno">  402</span>&#160;        <a class="code" href="class_s_p_h_1_1_diffusion_boundary_condtion.html">DiffusionBoundaryCondtion</a>(BodyType* body, BodyPartByParticleType* body_part)</div><div class="line"><a name="l00403"></a><span class="lineno">  403</span>&#160;            : <a class="code" href="class_s_p_h_1_1_part_dynamics_by_particle.html">DiffusionReactionConstraint</a>&lt;BodyType,</div><div class="line"><a name="l00404"></a><span class="lineno">  404</span>&#160;            <a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>, BodyPartByParticleType, <a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>&gt;(body, body_part) {}</div><div class="line"><a name="l00405"></a><span class="lineno">  405</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_diffusion_boundary_condtion.html">DiffusionBoundaryCondtion</a>() {};</div><div class="line"><a name="l00406"></a><span class="lineno">  406</span>&#160;</div><div class="line"><a name="l00407"></a><span class="lineno">  407</span>&#160;    };</div><div class="line"><a name="l00408"></a><span class="lineno">  408</span>&#160;</div><div class="line"><a name="l00413"></a><span class="lineno">  413</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00414"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_based_mapping.html">  414</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_diffusion_based_mapping.html">DiffusionBasedMapping</a> :</div><div class="line"><a name="l00415"></a><span class="lineno">  415</span>&#160;        <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_particle_dynamics_simple.html">DiffusionReactionSimple</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div><div class="line"><a name="l00416"></a><span class="lineno">  416</span>&#160;    {</div><div class="line"><a name="l00417"></a><span class="lineno">  417</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00418"></a><span class="lineno">  418</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> Update(<span class="keywordtype">size_t</span> index_particle_i, Real dt = 0.0) = 0;</div><div class="line"><a name="l00419"></a><span class="lineno">  419</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00420"></a><span class="lineno">  420</span>&#160;        <a class="code" href="class_s_p_h_1_1_diffusion_based_mapping.html">DiffusionBasedMapping</a>(BodyType* body)</div><div class="line"><a name="l00421"></a><span class="lineno">  421</span>&#160;            : <a class="code" href="class_s_p_h_1_1_particle_dynamics_simple.html">DiffusionReactionSimple&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</a>(body) {};</div><div class="line"><a name="l00422"></a><span class="lineno">  422</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_diffusion_based_mapping.html">DiffusionBasedMapping</a>() {};</div><div class="line"><a name="l00423"></a><span class="lineno">  423</span>&#160;    };</div><div class="line"><a name="l00424"></a><span class="lineno">  424</span>&#160;}</div><div class="ttc" id="class_s_p_h_1_1_neighborhood_html"><div class="ttname"><a href="class_s_p_h_1_1_neighborhood.html">SPH::Neighborhood</a></div><div class="ttdoc">A neighborhood around particle i. </div><div class="ttdef"><b>Definition:</b> neighbor_relation.h:77</div></div>
<div class="ttc" id="class_s_p_h_1_1_particle_dynamics_inner_with_update_html"><div class="ttname"><a href="class_s_p_h_1_1_particle_dynamics_inner_with_update.html">SPH::ParticleDynamicsInnerWithUpdate</a></div><div class="ttdoc">This class includes an initialization, an inner interaction and an update steps. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_algorithms.h:118</div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_difussion_species_html_a0e202b2a607b21d6c94075270217c852"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_difussion_species.html#a0e202b2a607b21d6c94075270217c852">SPH::RelaxationOfAllDifussionSpecies::updateDiffusionSpecies</a></div><div class="ttdeci">virtual void updateDiffusionSpecies(DiffusionReactionData &amp;diffusion_reaction_data_i, Real dt)</div><div class="ttdoc">Update all diffusion species. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:148</div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_reactions_backward_html_a7274653cfb4e8a753476dd247990f206"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_reactions_backward.html#a7274653cfb4e8a753476dd247990f206">SPH::RelaxationOfAllReactionsBackward::UpdateReactiveSpeciesBackward</a></div><div class="ttdeci">void UpdateReactiveSpeciesBackward(DiffusionReactionData &amp;diffusion_reaction_data_i, Real dt)</div><div class="ttdoc">Get change rate for all rective species by backward sweeping. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:366</div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_difussion_species_html"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_difussion_species.html">SPH::RelaxationOfAllDifussionSpecies</a></div><div class="ttdoc">Compute the diffusion relaxation process of all species. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:102</div></div>
<div class="ttc" id="class_s_p_h_1_1_s_p_h_body_inner_relation_html"><div class="ttname"><a href="class_s_p_h_1_1_s_p_h_body_inner_relation.html">SPH::SPHBodyInnerRelation</a></div><div class="ttdoc">The relation within a SPH body. </div><div class="ttdef"><b>Definition:</b> body_relation.h:65</div></div>
<div class="ttc" id="namespace_s_p_h_html_abae56fd7f25f13487c7943ce4681d0ce"><div class="ttname"><a href="namespace_s_p_h.html#abae56fd7f25f13487c7943ce4681d0ce">SPH::IndexVector</a></div><div class="ttdeci">StdVec&lt; size_t &gt; IndexVector</div><div class="ttdef"><b>Definition:</b> sph_data_conainers.h:30</div></div>
<div class="ttc" id="class_s_p_h_1_1_particle_dynamics_with_inner_configurations_html_a847144aa189dd161047be589b5b59507"><div class="ttname"><a href="class_s_p_h_1_1_particle_dynamics_with_inner_configurations.html#a847144aa189dd161047be589b5b59507">SPH::ParticleDynamicsWithInnerConfigurations::inner_configuration_</a></div><div class="ttdeci">ParticleConfiguration &amp; inner_configuration_</div><div class="ttdef"><b>Definition:</b> base_particle_dynamics.h:191</div></div>
<div class="ttc" id="class_s_p_h_1_1_neighborhood_html_a1e2d0d9c7af09e2ee0e58903b171902d"><div class="ttname"><a href="class_s_p_h_1_1_neighborhood.html#a1e2d0d9c7af09e2ee0e58903b171902d">SPH::Neighborhood::current_size_</a></div><div class="ttdeci">size_t current_size_</div><div class="ttdef"><b>Definition:</b> neighbor_relation.h:83</div></div>
<div class="ttc" id="class_s_p_h_1_1_particle_dynamics_simple_html"><div class="ttname"><a href="class_s_p_h_1_1_particle_dynamics_simple.html">SPH::ParticleDynamicsSimple</a></div><div class="ttdoc">Simple particle dynamics without considering particle interaction. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_algorithms.h:48</div></div>
<div class="ttc" id="diffusion__reaction__particles_8h_html"><div class="ttname"><a href="diffusion__reaction__particles_8h.html">diffusion_reaction_particles.h</a></div><div class="ttdoc">This is the derived class of diffusion reaction particles. </div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_1_1_runge_kutta_initialization_html"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_1_1_runge_kutta_initialization.html">SPH::RelaxationOfAllDiffusionSpeciesRK2::RungeKuttaInitialization</a></div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:208</div></div>
<div class="ttc" id="class_s_p_h_1_1_common_relation_html"><div class="ttname"><a href="class_s_p_h_1_1_common_relation.html">SPH::CommonRelation</a></div><div class="ttdoc">The common relation for a particle j around particle i. </div><div class="ttdef"><b>Definition:</b> neighbor_relation.h:42</div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_reactions_foward_html"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_reactions_foward.html">SPH::RelaxationOfAllReactionsFoward</a></div><div class="ttdoc">Compute the reaction process of all species by forward splitting. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:289</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_reaction_model_html_ac9370e5551fc733dccfa12e9364bb27d"><div class="ttname"><a href="class_s_p_h_1_1_base_reaction_model.html#ac9370e5551fc733dccfa12e9364bb27d">SPH::BaseReactionModel::get_loss_rates_</a></div><div class="ttdeci">StdVec&lt; ReactionFunctor &gt; get_loss_rates_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:199</div></div>
<div class="ttc" id="class_s_p_h_1_1_common_relation_html_a2fdbf618dfaaca3cf77176907c1e7ae0"><div class="ttname"><a href="class_s_p_h_1_1_common_relation.html#a2fdbf618dfaaca3cf77176907c1e7ae0">SPH::CommonRelation::dW_ij_</a></div><div class="ttdeci">Real dW_ij_</div><div class="ttdef"><b>Definition:</b> neighbor_relation.h:48</div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_html"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html">SPH::RelaxationOfAllDiffusionSpeciesRK2</a></div><div class="ttdoc">Compute the diffusion relaxation process of all species with second order Runge Kutta time stepping...</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:203</div></div>
<div class="ttc" id="class_s_p_h_1_1_particle_dynamics_html_a129036fc16e69eb21e69a259ca20036a"><div class="ttname"><a href="class_s_p_h_1_1_particle_dynamics.html#a129036fc16e69eb21e69a259ca20036a">SPH::ParticleDynamics&lt; void, BodyType, BaseParticlesType, BaseMaterialType &gt;::ParticleDynamics</a></div><div class="ttdeci">ParticleDynamics(SPHBody *body)</div><div class="ttdef"><b>Definition:</b> base_particle_dynamics.h:172</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_reaction_model_html_a910ab731d18d21e073360a0e837e9dc9"><div class="ttname"><a href="class_s_p_h_1_1_base_reaction_model.html#a910ab731d18d21e073360a0e837e9dc9">SPH::BaseReactionModel::get_production_rates_</a></div><div class="ttdeci">StdVec&lt; ReactionFunctor &gt; get_production_rates_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:197</div></div>
<div class="ttc" id="class_real_html"><div class="ttname"><a href="class_real.html">Real</a></div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_data_html_a9c9c5fa76e83b20f66c7eb961dea9b76"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_data.html#a9c9c5fa76e83b20f66c7eb961dea9b76">SPH::DiffusionReactionData::dspecies_dt_</a></div><div class="ttdeci">StdVec&lt; Real &gt; dspecies_dt_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:61</div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_1_1_runge_kutta2_stages2nd_stage_html_a93084988dfa7a46c43ef5e899e2e1b06"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_1_1_runge_kutta2_stages2nd_stage.html#a93084988dfa7a46c43ef5e899e2e1b06">SPH::RelaxationOfAllDiffusionSpeciesRK2::RungeKutta2Stages2ndStage::updateDiffusionSpecies</a></div><div class="ttdeci">virtual void updateDiffusionSpecies(DiffusionReactionData &amp;diffusion_reaction_data_i, Real dt) override</div><div class="ttdoc">Update all diffusion species. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:244</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_particles_type_html"><div class="ttname"><a href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a></div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_html_ac90349521ec2a782159bb2536722e3bb"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html#ac90349521ec2a782159bb2536722e3bb">SPH::RelaxationOfAllDiffusionSpeciesRK2::exec</a></div><div class="ttdeci">virtual void exec(Real dt=0.0) override</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:272</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_based_mapping_html"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_based_mapping.html">SPH::DiffusionBasedMapping</a></div><div class="ttdoc">Mapping inside of body according to diffusion. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:414</div></div>
<div class="ttc" id="class_s_p_h_1_1_get_diffusion_time_step_size_html"><div class="ttname"><a href="class_s_p_h_1_1_get_diffusion_time_step_size.html">SPH::GetDiffusionTimeStepSize</a></div><div class="ttdoc">Computing the acoustic time step size computing time step size. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:79</div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_reactions_foward_html_aceb02571347f79c52fb1b97870863a36"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_reactions_foward.html#aceb02571347f79c52fb1b97870863a36">SPH::RelaxationOfAllReactionsFoward::updateAReactionSpecies</a></div><div class="ttdeci">Real updateAReactionSpecies(Real input, Real production_rate, Real loss_rate, Real dt)</div><div class="ttdoc">Splitting scheme for directly computing one time step integeration for a species. ...</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:303</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_data_html"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_data.html">SPH::DiffusionReactionData</a></div><div class="ttdoc">Particles data for general diffusion/reaction problems. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:49</div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_1_1_runge_kutta2_stages2nd_stage_html"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_1_1_runge_kutta2_stages2nd_stage.html">SPH::RelaxationOfAllDiffusionSpeciesRK2::RungeKutta2Stages2ndStage</a></div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:240</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_data_html_a387eae85205f80dd35b898faee438ad5"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_data.html#a387eae85205f80dd35b898faee438ad5">SPH::DiffusionReactionData::species_n_</a></div><div class="ttdeci">StdVec&lt; Real &gt; species_n_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:54</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_reaction_model_html"><div class="ttname"><a href="class_s_p_h_1_1_base_reaction_model.html">SPH::BaseReactionModel</a></div><div class="ttdoc">Base class for all reaction models. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:184</div></div>
<div class="ttc" id="class_s_p_h_1_1_common_relation_html_a7c8fa7c04fd21a9668feade22912115b"><div class="ttname"><a href="class_s_p_h_1_1_common_relation.html#a7c8fa7c04fd21a9668feade22912115b">SPH::CommonRelation::j_</a></div><div class="ttdeci">size_t j_</div><div class="ttdef"><b>Definition:</b> neighbor_relation.h:52</div></div>
<div class="ttc" id="class_s_p_h_1_1_get_diffusion_time_step_size_html_abbafdb225bf35578cb3d8d891f54b1e9"><div class="ttname"><a href="class_s_p_h_1_1_get_diffusion_time_step_size.html#abbafdb225bf35578cb3d8d891f54b1e9">SPH::GetDiffusionTimeStepSize::exec</a></div><div class="ttdeci">virtual Real exec(Real dt=0.0) override</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:93</div></div>
<div class="ttc" id="class_s_p_h_1_1_common_relation_html_a3e4dd95b6dbe984aeb19c2e4977fd161"><div class="ttname"><a href="class_s_p_h_1_1_common_relation.html#a3e4dd95b6dbe984aeb19c2e4977fd161">SPH::CommonRelation::e_ij_</a></div><div class="ttdeci">Vecd e_ij_</div><div class="ttdef"><b>Definition:</b> neighbor_relation.h:46</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_particles_html_ace9886026ada5948e27c14a0ce827b2f"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html#ace9886026ada5948e27c14a0ce827b2f">SPH::DiffusionReactionParticles::diffusion_reaction_data_</a></div><div class="ttdeci">StdLargeVec&lt; DiffusionReactionData &gt; diffusion_reaction_data_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:77</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_reaction_model_html_a5d7b0f83c36dd9b3efd1c5a8c74f2073"><div class="ttname"><a href="class_s_p_h_1_1_base_reaction_model.html#a5d7b0f83c36dd9b3efd1c5a8c74f2073">SPH::BaseReactionModel::reactive_species_</a></div><div class="ttdeci">IndexVector reactive_species_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:192</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_data_html_a225749466f115c22bae74deb18140ce7"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_data.html#a225749466f115c22bae74deb18140ce7">SPH::DiffusionReactionData::species_s_</a></div><div class="ttdeci">StdVec&lt; Real &gt; species_s_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:59</div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_reactions_foward_html_a343795cd46824a0595121c07a5480662"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_reactions_foward.html#a343795cd46824a0595121c07a5480662">SPH::RelaxationOfAllReactionsFoward::UpdateReactiveSpeciesForward</a></div><div class="ttdeci">void UpdateReactiveSpeciesForward(DiffusionReactionData &amp;diffusion_reaction_data_i, Real dt)</div><div class="ttdoc">Get change rate for all rective species by backward sweeping. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:312</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_boundary_condtion_html"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_boundary_condtion.html">SPH::DiffusionBoundaryCondtion</a></div><div class="ttdoc">set boudary condition for diffusion problem </div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:398</div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_difussion_species_html_ab82d1578c5e8cbabe687e0af9810fbd1"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_difussion_species.html#ab82d1578c5e8cbabe687e0af9810fbd1">SPH::RelaxationOfAllDifussionSpecies::getDiffusionChangeRate</a></div><div class="ttdeci">void getDiffusionChangeRate(size_t particle_i, size_t particle_j, Vecd &amp;e_ij, Real surface_area_ij, DiffusionReactionData &amp;diffusion_reaction_data_i, DiffusionReactionData &amp;diffusion_reaction_data_j)</div><div class="ttdoc">Get change rate for all diffusion species. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:130</div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_reactions_backward_html"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_reactions_backward.html">SPH::RelaxationOfAllReactionsBackward</a></div><div class="ttdoc">Compute the reaction process of all species by backward splitting. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:342</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_material_type_html"><div class="ttname"><a href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a></div></div>
<div class="ttc" id="class_s_p_h_1_1_part_dynamics_by_particle_html"><div class="ttname"><a href="class_s_p_h_1_1_part_dynamics_by_particle.html">SPH::PartDynamicsByParticle</a></div><div class="ttdoc">Imposing Lagrangian constrain to a body. That is the constrained particles will be the same during th...</div><div class="ttdef"><b>Definition:</b> particle_dynamics_bodypart.h:24</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_particles_html"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html">SPH::DiffusionReactionParticles</a></div><div class="ttdoc">A group of particles with diffusion or/and reactions particle data. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:45</div></div>
<div class="ttc" id="class_s_p_h_1_1_s_p_h_body_html"><div class="ttname"><a href="class_s_p_h_1_1_s_p_h_body.html">SPH::SPHBody</a></div><div class="ttdoc">SPHBody is a base body with basic data and functions. Its derived class can be a real fluid body...</div><div class="ttdef"><b>Definition:</b> base_body.h:73</div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_difussion_species_html_ad1cd798d759a665cc40131c773aa581f"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_difussion_species.html#ad1cd798d759a665cc40131c773aa581f">SPH::RelaxationOfAllDifussionSpecies::initializeDiffusionChangeRate</a></div><div class="ttdeci">void initializeDiffusionChangeRate(DiffusionReactionData &amp;diffusion_reaction_data_i)</div><div class="ttdoc">Initialize change rate to zero for all diffusion species. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:112</div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_reactions_backward_html_a70a0ba2530a5fc9bc2e99340b36ba00c"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_reactions_backward.html#a70a0ba2530a5fc9bc2e99340b36ba00c">SPH::RelaxationOfAllReactionsBackward::updateAReactionSpecies</a></div><div class="ttdeci">Real updateAReactionSpecies(Real input, Real production_rate, Real loss_rate, Real dt)</div><div class="ttdoc">Splitting scheme for directly computing one time step integeration for a species. ...</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:356</div></div>
<div class="ttc" id="class_s_p_h_1_1_common_relation_html_a1a3bacd903ac2c946e196610b634bcaf"><div class="ttname"><a href="class_s_p_h_1_1_common_relation.html#a1a3bacd903ac2c946e196610b634bcaf">SPH::CommonRelation::r_ij_</a></div><div class="ttdeci">Real r_ij_</div><div class="ttdef"><b>Definition:</b> neighbor_relation.h:50</div></div>
<div class="ttc" id="namespace_s_p_h_html_aa1b1a469a853a78ec95f6bf7b3ded9f4"><div class="ttname"><a href="namespace_s_p_h.html#aa1b1a469a853a78ec95f6bf7b3ded9f4">SPH::CommonRelationList</a></div><div class="ttdeci">StdLargeVec&lt; CommonRelation &gt; CommonRelationList</div><div class="ttdef"><b>Definition:</b> neighbor_relation.h:69</div></div>
<div class="ttc" id="namespace_s_p_h_html"><div class="ttname"><a href="namespace_s_p_h.html">SPH</a></div><div class="ttdef"><b>Definition:</b> base_body_supplementary.cpp:11</div></div>
<div class="ttc" id="class_s_p_h_1_1_particle_dynamics_html"><div class="ttname"><a href="class_s_p_h_1_1_particle_dynamics.html">SPH::ParticleDynamics</a></div><div class="ttdoc">Particle dynamics base class Bodies are involved the dynamics of a designated body and the bodies int...</div><div class="ttdef"><b>Definition:</b> base_particle_dynamics.h:159</div></div>
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